Contacts of the strand formed by residues 62 - 66 (chain A) in PDB entry 2NS2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ARG 5.8 1.7 + - - -
26A ARG 4.9 5.7 + - - -
28A ILE* 3.6 29.7 - - + +
29A VAL* 4.8 2.5 - - + -
51A VAL* 3.8 14.8 - - + -
53A ASP 3.3 16.4 - - - +
54A GLN* 3.6 41.1 + - + -
59A PRO 4.3 5.2 + - - -
60A SER 3.6 15.9 - - - -
61A LEU* 1.3 74.4 - - - +
63A LEU* 1.3 64.3 + - - +
64A ILE* 3.6 7.6 - - + +
73A TYR 3.5 0.7 - - - +
74A GLY* 3.1 5.2 - - - -
75A LEU 2.9 37.4 + - - +
77A LEU* 3.8 27.1 - - + -
78A ASN* 3.5 30.8 + - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.9 1.4 - - - +
52A LEU* 2.9 30.7 + - + -
53A ASP* 3.0 35.7 + - + +
55A VAL* 4.3 12.6 - - + -
61A LEU* 4.9 2.0 - - + -
62A TYR* 1.3 80.9 - - - +
64A ILE* 1.3 62.0 + - - +
72A VAL* 4.1 12.8 - - + -
73A TYR 3.1 3.4 - - - +
74A GLY* 3.9 4.9 - - - -
142A TYR* 4.4 13.7 - - - +
151A LEU* 4.9 2.7 - - + -
208A ILE* 4.3 14.8 - - + -
209A HIS* 4.5 14.1 - - + -
219A PHE* 4.8 10.8 - - + -
228A ILE* 3.8 30.1 - - + -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.3 7.2 - - + -
49A GLY 4.2 1.6 - - - -
50A THR 3.3 26.0 - - - +
51A VAL* 4.5 4.5 - - + -
52A LEU* 4.1 4.5 - - - -
62A TYR* 3.6 22.4 - - + +
63A LEU* 1.3 76.7 - - - +
65A LYS* 1.3 65.5 + - - +
66A TYR* 3.5 51.0 + - + +
71A CYS 4.5 0.5 - - - +
72A VAL* 3.7 3.5 - - - +
73A TYR* 2.7 41.4 + - - +
75A LEU* 4.1 10.1 - - + +
77A LEU* 4.0 29.4 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLY* 3.1 1.7 - - - -
50A THR* 2.7 35.2 + - - +
52A LEU* 4.0 8.3 - - + +
64A ILE* 1.3 72.1 - - - +
66A TYR* 1.3 72.6 + - - +
67A ASP* 4.7 2.8 - - - +
68A GLY 4.9 2.8 - - - +
69A PHE 2.7 29.7 + - - +
70A ASP* 4.3 8.5 + - - +
71A CYS 4.8 4.5 - - - +
72A VAL* 5.1 2.7 - - + +
137A MET* 3.9 30.3 - - + +
140A TRP* 4.0 23.0 - - - -
153A MET* 3.8 48.9 - - + -
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.3 3.1 - - + +
35A HIS* 2.7 36.2 + + - -
47A TRP* 3.7 31.9 - + + -
48A LYS 3.5 18.4 - - - +
49A GLY* 3.9 7.2 - - - -
64A ILE* 3.5 31.1 + - + +
65A LYS* 1.3 96.8 + - - +
67A ASP* 1.3 69.9 + - - +
69A PHE* 3.2 43.1 + + + +
71A CYS 5.2 1.0 + - - -
73A TYR* 3.8 23.8 - + + -
75A LEU* 3.5 7.0 - - + +
77A LEU* 3.4 18.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il